Merge branch 'release_23.2' into dev

packages/app/HISTORY.rst

@@ -4,11 +4,35 @@ History
 .. to_doc
 
 ---------
-23.2.dev0
+23.3.dev0
 ---------
 
 
 
+-------------------
+23.1.2 (2023-11-29)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Fix unbound ``runner`` variable when there is an error in the job config by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16906 <https://github.com/galaxyproject/galaxy/pull/16906>`_
+* Fix discarded dataset ordering in Storage Dashboard by `@davelopez <https://github.com/davelopez>`_ in `#16929 <https://github.com/galaxyproject/galaxy/pull/16929>`_
+* Include owner's annotation when exporting workflow by `@dannon <https://github.com/dannon>`_ in `#16930 <https://github.com/galaxyproject/galaxy/pull/16930>`_
+* Skip state filtering in ``__MERGE_COLLECTION__`` tool  by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16937 <https://github.com/galaxyproject/galaxy/pull/16937>`_
+* Prevent Singular external auth users from disconnecting identity by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#16961 <https://github.com/galaxyproject/galaxy/pull/16961>`_
+* Prevent workflow submission with missing input values by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17048 <https://github.com/galaxyproject/galaxy/pull/17048>`_
+* Fix extra files collection if using ``store_by="id"`` and `outputs_to_working_directory` by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17067 <https://github.com/galaxyproject/galaxy/pull/17067>`_
+* Remove rollback from ``__check_jobs_at_startup`` by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17085 <https://github.com/galaxyproject/galaxy/pull/17085>`_
+
+============
+Enhancements
+============
+
+* Improve invocation error reporting by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16917 <https://github.com/galaxyproject/galaxy/pull/16917>`_
+
 -------------------
 23.1.1 (2023-10-23)
 -------------------
@@ -158,6 +182,7 @@ Other changes
 Bug fixes
 =========
 
+* 
 * Fix upload paramfile handling (for real user setups) by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#16504 <https://github.com/galaxyproject/galaxy/pull/16504>`_
 * Fix extra files path handling by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16541 <https://github.com/galaxyproject/galaxy/pull/16541>`_
 * Make sure job_wrapper uses a consistent metadata strategy by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16569 <https://github.com/galaxyproject/galaxy/pull/16569>`_
@@ -171,6 +196,7 @@ Bug fixes
 Enhancements
 ============
 
+* 
 * Update pulsar client library to 0.15.5 by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16701 <https://github.com/galaxyproject/galaxy/pull/16701>`_
 
 -------------------
@@ -182,6 +208,7 @@ Enhancements
 Bug fixes
 =========
 
+* 
 * 
 * Skip installing npm/yarn if available, fix conditional dependency parsing, create virtualenv via conda when conda active by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#16403 <https://github.com/galaxyproject/galaxy/pull/16403>`_
 * Fix test discovery in vscode by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16413 <https://github.com/galaxyproject/galaxy/pull/16413>`_
@@ -196,6 +223,7 @@ Bug fixes
 Bug fixes
 =========
 
+* 
 * 
 * 
 * Fix default when statement evaluation by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16332 <https://github.com/galaxyproject/galaxy/pull/16332>`_
@@ -213,19 +241,22 @@ Bug fixes
 * 
 * 
 * 
+* 
 * Bump galaxy-release-util version to 0.1.2 by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16241 <https://github.com/galaxyproject/galaxy/pull/16241>`_
 
 ============
 Enhancements
 ============
 
+* 
 * 
 * When importing tool data bundles, use the first loc file for the matching table by `@natefoo <https://github.com/natefoo>`_ in `#16247 <https://github.com/galaxyproject/galaxy/pull/16247>`_
 
 =============
 Other changes
 =============
 
+* 
 * Forward port of slugify username received from oidc by `@nuwang <https://github.com/nuwang>`_ in `#16271 <https://github.com/galaxyproject/galaxy/pull/16271>`_
 
 -------------------
@@ -241,6 +272,7 @@ Bug fixes
 * 
 * 
 * 
+* 
 * Fix ``Text File Busy`` errors at the source by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16212 <https://github.com/galaxyproject/galaxy/pull/16212>`_
 
 ============
@@ -251,6 +283,7 @@ Enhancements
 * 
 * 
 * 
+* 
 * Point release deps fixes and docs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16214 <https://github.com/galaxyproject/galaxy/pull/16214>`_
 * Use galaxy-release-util to upload python packages by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16240 <https://github.com/galaxyproject/galaxy/pull/16240>`_
 
@@ -268,6 +301,7 @@ Bug fixes
 * 
 * 
 * 
+* 
 * Display DCE in job parameter component, allow rerunning with DCE input by `@mvdbeek <https://github.com/mvdbeek>`_ in `#15744 <https://github.com/galaxyproject/galaxy/pull/15744>`_
 * Fix mixed outputs_to_working_directory pulsar destinations by `@mvdbeek <https://github.com/mvdbeek>`_ in `#15927 <https://github.com/galaxyproject/galaxy/pull/15927>`_
 * Update Gravity to 1.0.3 by `@natefoo <https://github.com/natefoo>`_ in `#15939 <https://github.com/galaxyproject/galaxy/pull/15939>`_
@@ -295,6 +329,7 @@ Other changes
 * 
 * 
 * 
+* 
 * Startup fix when tool removed between reboot by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16175 <https://github.com/galaxyproject/galaxy/pull/16175>`_
 
 -------------------

packages/auth/HISTORY.rst

@@ -4,11 +4,17 @@ History
 .. to_doc
 
 ---------
-23.2.dev0
+23.3.dev0
 ---------
 
 
 
+-------------------
+23.1.2 (2023-11-29)
+-------------------
+
+No recorded changes since last release
+
 -------------------
 23.1.1 (2023-10-23)
 -------------------

packages/config/HISTORY.rst

@@ -4,11 +4,29 @@ History
 .. to_doc
 
 ---------
-23.2.dev0
+23.3.dev0
 ---------
 
 
 
+-------------------
+23.1.2 (2023-11-29)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Prevent Singular external auth users from disconnecting identity by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#16961 <https://github.com/galaxyproject/galaxy/pull/16961>`_
+* Set correct tool_path for packaged galaxy by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17102 <https://github.com/galaxyproject/galaxy/pull/17102>`_
+
+============
+Enhancements
+============
+
+* Add support for larch datatypes by `@patrick-austin <https://github.com/patrick-austin>`_ in `#17080 <https://github.com/galaxyproject/galaxy/pull/17080>`_
+
 -------------------
 23.1.1 (2023-10-23)
 -------------------
@@ -71,6 +89,7 @@ No recorded changes since last release
 Bug fixes
 =========
 
+* 
 * Minor bug fix for default mail templates by `@neoformit <https://github.com/neoformit>`_ in `#16362 <https://github.com/galaxyproject/galaxy/pull/16362>`_
 
 -------------------
@@ -100,6 +119,7 @@ No recorded changes since last release
 Bug fixes
 =========
 
+* 
 * 
 * 
 * Change default watchdog inotify_buffer log level to info by `@mvdbeek <https://github.com/mvdbeek>`_ in `#15967 <https://github.com/galaxyproject/galaxy/pull/15967>`_
@@ -108,6 +128,7 @@ Bug fixes
 Enhancements
 ============
 
+* 
 * Add ``ca_certs`` option for sentry client by `@mvdbeek <https://github.com/mvdbeek>`_ in `#15943 <https://github.com/galaxyproject/galaxy/pull/15943>`_
 
 -------------------

packages/data/HISTORY.rst

@@ -4,11 +4,34 @@ History
 .. to_doc
 
 ---------
-23.2.dev0
+23.3.dev0
 ---------
 
 
 
+-------------------
+23.1.2 (2023-11-29)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Skip change_datatype things if we're not actually changing the extension by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16931 <https://github.com/galaxyproject/galaxy/pull/16931>`_
+* Fix copying metadata to copied job outputs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17007 <https://github.com/galaxyproject/galaxy/pull/17007>`_
+* Update tar_to_directory dependency by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17009 <https://github.com/galaxyproject/galaxy/pull/17009>`_
+* Assert that ``DatasetCollectioElement`` has an associated object by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17071 <https://github.com/galaxyproject/galaxy/pull/17071>`_
+* Fix input dates in notifications: consider timezone offset by `@davelopez <https://github.com/davelopez>`_ in `#17088 <https://github.com/galaxyproject/galaxy/pull/17088>`_
+* Allow relative URLs in broadcasts action links by `@davelopez <https://github.com/davelopez>`_ in `#17093 <https://github.com/galaxyproject/galaxy/pull/17093>`_
+
+============
+Enhancements
+============
+
+* Improve invocation error reporting by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16917 <https://github.com/galaxyproject/galaxy/pull/16917>`_
+* Add support for larch datatypes by `@patrick-austin <https://github.com/patrick-austin>`_ in `#17080 <https://github.com/galaxyproject/galaxy/pull/17080>`_
+
 -------------------
 23.1.1 (2023-10-23)
 -------------------
@@ -106,6 +129,7 @@ Other changes
 Bug fixes
 =========
 
+* 
 * Fix extra files path handling by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16541 <https://github.com/galaxyproject/galaxy/pull/16541>`_
 * Don't fail invocation message without dependent_workflow_step_id by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16628 <https://github.com/galaxyproject/galaxy/pull/16628>`_
 
@@ -118,6 +142,7 @@ Bug fixes
 Bug fixes
 =========
 
+* 
 * 
 * Copy when_expression when copying workflow step by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16377 <https://github.com/galaxyproject/galaxy/pull/16377>`_
 
@@ -148,6 +173,7 @@ No recorded changes since last release
 Bug fixes
 =========
 
+* 
 * 
 * 
 * Display DCE in job parameter component, allow rerunning with DCE input by `@mvdbeek <https://github.com/mvdbeek>`_ in `#15744 <https://github.com/galaxyproject/galaxy/pull/15744>`_

packages/files/HISTORY.rst

@@ -4,11 +4,22 @@ History
 .. to_doc
 
 ---------
-23.2.dev0
+23.3.dev0
 ---------
 
 
 
+-------------------
+23.1.2 (2023-11-29)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Implement missing upload for S3 file sources by `@davelopez <https://github.com/davelopez>`_ in `#17100 <https://github.com/galaxyproject/galaxy/pull/17100>`_
+
 -------------------
 23.1.1 (2023-10-23)
 -------------------
@@ -62,6 +73,7 @@ No recorded changes since last release
 Bug fixes
 =========
 
+* 
 * Fix dropbox import to support newer versions by `@nuwang <https://github.com/nuwang>`_ in `#16239 <https://github.com/galaxyproject/galaxy/pull/16239>`_
 
 -------------------

packages/job_execution/HISTORY.rst

@@ -4,11 +4,24 @@ History
 .. to_doc
 
 ---------
-23.2.dev0
+23.3.dev0
 ---------
 
 
 
+-------------------
+23.1.2 (2023-11-29)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Fix library import from path linking files by `@davelopez <https://github.com/davelopez>`_ in `#16919 <https://github.com/galaxyproject/galaxy/pull/16919>`_
+* Don't store job in JobIO instance attributes by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16965 <https://github.com/galaxyproject/galaxy/pull/16965>`_
+* Fix extra files collection if using ``store_by="id"`` and `outputs_to_working_directory` by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17067 <https://github.com/galaxyproject/galaxy/pull/17067>`_
+
 -------------------
 23.1.1 (2023-10-23)
 -------------------
@@ -46,6 +59,7 @@ Enhancements
 Bug fixes
 =========
 
+* 
 * Fix extra files path handling by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16541 <https://github.com/galaxyproject/galaxy/pull/16541>`_
 * Make sure job_wrapper uses a consistent metadata strategy by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16569 <https://github.com/galaxyproject/galaxy/pull/16569>`_
 * Fixes for extra files handling and cached object stores  by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16595 <https://github.com/galaxyproject/galaxy/pull/16595>`_

packages/job_metrics/HISTORY.rst

@@ -4,11 +4,17 @@ History
 .. to_doc
 
 ---------
-23.2.dev0
+23.3.dev0
 ---------
 
 
 
+-------------------
+23.1.2 (2023-11-29)
+-------------------
+
+No recorded changes since last release
+
 -------------------
 23.1.1 (2023-10-23)
 -------------------

packages/navigation/HISTORY.rst

@@ -4,11 +4,17 @@ History
 .. to_doc
 
 ---------
-23.2.dev0
+23.3.dev0
 ---------
 
 
 
+-------------------
+23.1.2 (2023-11-29)
+-------------------
+
+No recorded changes since last release
+
 -------------------
 23.1.1 (2023-10-23)
 -------------------

packages/objectstore/HISTORY.rst

@@ -4,11 +4,17 @@ History
 .. to_doc
 
 ---------
-23.2.dev0
+23.3.dev0
 ---------
 
 
 
+-------------------
+23.1.2 (2023-11-29)
+-------------------
+
+No recorded changes since last release
+
 -------------------
 23.1.1 (2023-10-23)
 -------------------
@@ -49,6 +55,7 @@ Other changes
 Bug fixes
 =========
 
+* 
 * Fix extra files path handling by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16541 <https://github.com/galaxyproject/galaxy/pull/16541>`_
 * Fixes for extra files handling and cached object stores  by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16595 <https://github.com/galaxyproject/galaxy/pull/16595>`_